I think only olneyce can explain exactly what he meant, but I'll take a stab at your comments.
Yeah, it's pretty common to overestimate Villages and not get enough money no matter how good you get. Just remember you need to buy Provinces in the end, and a fancy engine is only functioning to a situation where you can do that (or buy out piles and end on a low score, whatever) so you do need some way to gain or buy cards.
I'll be honest, I'm not sure what olneyce means specifically by good vs bad trashing, but I would guess he means 'good' trashing cards like Chapel/Steward/Apprentice vs 'bad' ones like Lookout/Transmute. While I am not going to be one to question a better player's advice, I probably wouldn't use those terms. I'd prefer cursers > money > trashing that fits your engine plan.
Chapel is only the best trasher if it's the best trasher in the particular Kingdom. Sometimes Ambassador or Steward fit the available cards better. There are games where you do not want a terminal trasher like it, though they may be few and far between.
I think it is best not to even think of Rats as a trasher. You aren't eliminating a card from your deck, you're just gaining a Rats (that is, unless Rats are out, which will happen too late to use Rats as a true trasher). Rats is more like a balloon you want to pop with your Salvager instead of popping Copper it ate.